Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate YP_002826921.1 NGR_c24100 dihydroxy-acid dehydratase
Query= curated2:Q8TW40 (549 letters) >NCBI__GCF_000018545.1:YP_002826921.1 Length = 608 Score = 356 bits (913), Expect = e-102 Identities = 224/544 (41%), Positives = 310/544 (56%), Gaps = 17/544 (3%) Query: 15 HRALLRACGLTDEEMD-RPFVAVVNTYSEVVPGHMHLDKVTEAVKAGIRMAGGVPFEVET 73 HR+ ++ GL + D RP + + NT+SE+ P + HL + E VK G+ AGG P E Sbjct: 54 HRSWMKNQGLPADTFDGRPIIGICNTWSELTPCNAHLRDLAERVKRGVYEAGGFPVEFPV 113 Query: 74 IALCDGIAMNTPGMKYSLPSRELVADTIETVIEAHRFDGFVAIVSCDKMVPGALMAAARL 133 + + T M R L A +E I + DG V + CDK P LM AA + Sbjct: 114 FSTGESTLRPTAMM-----FRNLAAMDVEESIRGNPVDGVVLLGGCDKTTPSLLMGAASV 168 Query: 134 DLPAAIVTGGPMEPGCVDGERVDLIDA-FEAVGAYEEGEISEEELEELEQRACPGPGSCA 192 D+PA +V+GGPM G G+ V A ++ + GE+S EE + EQ GSC Sbjct: 169 DIPAIVVSGGPMLNGKWRGKDVGSGTAIWQFSEMVKSGEMSLEEFMDAEQGMARSAGSCM 228 Query: 193 GMFTANTMACMTEVLGMSEFNCAATPATEAEKLRVAKLTGMRIVEAIEEGITARDVLTRE 252 M TA+TMA M E LGM+ AA PA +A + +++LTG RIVE ++E + D+LT++ Sbjct: 229 TMGTASTMASMAEALGMTLSGNAAIPAVDARRRVMSQLTGRRIVEMVKEDLRPSDILTKQ 288 Query: 253 AFLDAIRVDMALGGSTNTVLHLLAIAREADVELSLDDFDELSRETPHLCAMRPGGPYTMR 312 AF +AIRV+ A+GGSTN VLHLLA+A V+LSLDD+D L R+ P + ++P G Y M Sbjct: 289 AFENAIRVNGAVGGSTNAVLHLLALAGRIGVDLSLDDWDRLGRDVPTIVNLQPSGKYLME 348 Query: 313 DLYEAGGVPAVMKELADD--LHLDRIDFAGRSMRERVERTEVKDREVIRPKEDPVHEEGG 370 + Y AGG+P V+K +A+ LH D I +G ++ V + +VI PKE + + GG Sbjct: 349 EFYYAGGLPVVIKAVAEMGLLHNDAITVSGDTIWNDVRGVTNYNEDVILPKEKALTKSGG 408 Query: 371 IVVLYGNLAPKGAVIKTAALSEEMYEHEGPAVVFDSEEEATEAILGGDIDPGD--VVVIR 428 I VL GNLAP+GAV+K ++ S + +H+G AVVF+S E+ I D+D + V+V++ Sbjct: 409 IAVLRGNLAPRGAVLKPSSASPHLMQHKGRAVVFESIEDYHARINREDLDIDETCVMVLK 468 Query: 429 YEGPAGGPGMRE---MLTPTAALCGMGLDDSVALVTDGRFSGGTRGPCVGHVSPEAYRGG 485 Y GP G PGM E M P L G+ D + L +D R SG G + H +PEA GG Sbjct: 469 YCGPKGYPGMAEVGNMGLPPKVL-KKGITDMIRL-SDARMSGTAYGTVILHTAPEAAEGG 526 Query: 486 PIAVVEEGDTIRLDVRERRLEVDVEDEELEARLEEWEPPEDEVT-GYLRRYRELVRGADE 544 P+AVVE GD I +D+ R L + V DEEL R W P +T GY Y + V AD Sbjct: 527 PLAVVENGDLIEVDIPNRTLHLHVSDEELARRRAAWVSPVKPLTGGYGGLYIKTVMQADT 586 Query: 545 GAVL 548 GA L Sbjct: 587 GADL 590 Lambda K H 0.317 0.137 0.396 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 839 Number of extensions: 37 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 549 Length of database: 608 Length adjustment: 36 Effective length of query: 513 Effective length of database: 572 Effective search space: 293436 Effective search space used: 293436 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory